


After Cobra Rises

by STARS_NEMESIS



Category: G. I. Joe - All Media Types, GI Joe - Fandom
Genre: GI Joe - Freeform, Gen, Ninja
Language: English
Status: In-Progress
Published: 2013-04-13
Updated: 2013-04-12
Packaged: 2017-12-08 07:58:45
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 7,069
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/758973
Author URL: https://archiveofourown.org/users/STARS_NEMESIS/pseuds/STARS_NEMESIS
Summary: <blockquote class="userstuff">
              <p>Set after the film. Storm Shadow survives and realises a lie. He goes to the only person who can help, His Sword Brother, Snake Eyes. Up to you if you want to read. Storm Shadow and Snake Eyes Main, with other chacters.</p>
            </blockquote>





	1. Chapter 1

Storm Shadow survived the wounds he received from his sword brother. His wounds were healed by the nanomites that existed in his body. However something felt different to him. As he crawled through a COBRA base, he realized that his memories had been tampered with due to the nanomites. He also realized that the only person who could have done this to him was the man now known as the Cobra Commander. That was when he decided that he would try and get as much information to the Joes. This led him to the COBRA base. He had just managed to send a message to Snake Eyes when a group on neo-vipers knocked him unconscious and took him to see Zartan who was the acting chief as both the Commander and Destro were not there and the Baroness had betrayed the COBRA organization.

At the GI Joe headquarters Snake Eyes had just received a message and a large amount of data from the COBRA organization. He was fairly certain he knew who the message had come from as it had been signed with the initials, TSA. It also surprised him as he was almost certain that the person was dead. The data had come with an apology and a plea for help. With the note and data in hand, Snake Eyes asked for a meeting with his team and General Hawk. The meeting began and Snake Eyes gestured to what had been sent to him. The other team members were intrigued by the plans that COBRA had made. What captured their eyes the most was the design of a mechanical suit that would cause harm to the wearer. They studied the plans and soon realized that the suit was made for torture purposes. The person in the suit would be an innocent but would get the blame if they were discovered. They knew that if this suit should ever appear they would have to take care as the person inside was not in control of the suit. The COBRA soldiers would still be able to control it from their base.

It had been several days since Storm Shadow had been captured. Every day had been the same. He had been tortured and mercilessly beaten for his betrayal to the organization. Finally Zartan decided that he would use the new device that had been created by the Commander before his capture. He was going to use the mechanical suit and get payback at the GI Joes by deploying it in America.

Storm Shadow who was in an extremely weakened condition due to his beatings and malnourishment was near unconsciousness when he was placed in the suit. The suit had a dozen needles that were covered in many different toxins, but also drugs that kept him awake so that he could feel every pain that was inflicted on the machine and the drugs that would course through his body like it would be on fire…

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The GI Joes were urgently called for a meeting the next day at 0915 hours. As they met up in the briefing room, they were told by General Hawk that the mechanical suit that they had been studying had turned up in the capital in America. They were deployed within half an hour. Hawk reminded them that the person inside was innocent and to try and save them as well as the civilians.

The team arrived in America within a matter of hours and went to confront the battle suit.

Storm Shadow could only endure the pain as he saw the GI Joes vain efforts to stop the machine.

"Please just stop. Just kill me, please." He begged in his mind.

He knew his clan would not be happy with his thoughts as ninja were trained to endure pain. But the amount of pain he was in was killing him, more so than any other wound he had ever received. Suddenly the machine stopped.

Snake Eyes leapt onto the back of the suit and jammed a knife into the control matrix. This stopped the machine from receiving contact with the COBRA base. He flipped off the machine and stood in front with the other Joes as they waited for it to open. Then it slowly started to open and all the Joes, including Snake Eyes were astounded when Storm Shadow staggered out. His clothes were in tatters and he had deep cuts, bruises, lacerations, needle marks and many more signs of trauma. He blinked at them and then staggered towards Snake Eyes. All the Joes except Snake Eyes tensed forgetting that Storm Shadow was in no condition to attack them.

"Brother…" Storm Shadow gasped as he fell into Snake Eyes, who opened his arms to catch the falling Storm Shadow.

"We need to take him back to base. He needs medical attention. Snake Eyes signed to his teammates.

"Snake, You do realize who this is don't you?" Scarlett asked as she looked down upon the unconscious ninja.

Yes. But did you forget that he has been tortured in that device. I am also certain that he sent that information to me. Please. We need to get him back and get him help.

The Joes looked at each other and then Duke contacted Hawk and updated him on the situation. Hawk agreed with Snake Eyes and ordered for them to bring Storm Shadow so that they could find out.

Duke agreed and told the other Joes. Within minutes they were in their jet and on their way back to the pit. On the way they treated what injuries they could. They noticed that Snake Eyes stayed close. Duke made a mental note to ask about the 2 later when Storm Shadow was better and this mess was cleared up.

The journey back to the pit was short. When they got back, Storm Shadow was immediately rushed into the hospital. The Doc and Lifeline worked on him for over 4 hours. His list of wounds was extensive and they made detailed notes so that they could tell the Joes and Hawk exactly what Storm Shadow had gone through and for how long.

Meanwhile in the debriefing room Hawk was with the Joes awaiting news. However none were more agitated than Snake Eyes who was pacing back and forth.

Finally Doc and Lifeline entered saying that Storm Shadow would be fine and that he would make a full recovery and that he was asleep for the moment.

May I sit with him? Snake gestured to Hawk and the Doc.

The Doc nodded yes and Hawk seeing how important this was for Snake agreed.

Snake walked into the hospital bay and sat by Storm Shadows side. He watched as the man breathed in and out and wondered what had befallen him.

Almost a week passed before Storm Shadow woke. When he did the first thing he saw was Snake Eyes. Snake was sprawled partly across his bed and it was obvious that the ninja was asleep. Storm Shadow smiled as he looked down at him and remembered that they had eventually become extremely close friends after he had discovered the boy breaking in. They had been inseparable. His mind was fighting the nanomites that had changed his memories and now remembered his past and that the two really had been like brothers and he remembered the true reason why he had joined COBRA.

He still smiled down at his friend. He was so engrossed with his thoughts that he did not notice Doc and Lifeline had appeared and were watching. Both made a note to tell Hawk about this.

Doc and Lifeline walked over and as they did, Snake Eyes awoke and looked towards them. Then he looked at Storm Shadow and jumped up when he saw that he was awake.

He unashamedly threw his arms around Storm Shadows neck and Storm Shadow returned the hug as enthusiastically, even though it caused him pain. Doc and Lifeline laughed and moved the excited Snake Eyes aside so that they could check their work. Then they asked if Storm would be up to talking with the General and some of the other Joes, including the Baroness. Storm Shadow agreed as he knew that he would have to explain himself at some point.

Hawk and the Joes entered. The Joes included Duke, Ripcord, Scarlett and Snake Eyes who had stayed with Storm. Baroness was also present and was glaring at the bed ridden ninja.

Hawk sat himself down and looked at Storm Shadow.

"So tell us how you got involved with COBRA and what you are doing here now and what you want." Hawk ordered.

Storm Shadow nodded and looked towards Snake Eyes.

"My story starts several years ago when I was a student with the Arashikage clan. Snake also became a member after he broke in to get some food. Our master was killed." Here Storm Shadow stopped and looked at Snake Eyes who had stiffened.

"I never killed our master, Snake. I saw someone there and ran over and I saw them put the sword in our master. I chased after him. I spent the next few years tracking the assassin. The trail eventually led me to COBRA. I infiltrated the organization so that I could find who killed our master. The Commander injected me with his nanomites and changed my memories, so that I believed you were my enemy. You know that I would never intentionally hurt you. Don't you Snake?" Storm asked fearing the answer.

Snake nodded and they could all see that the story made sense.

"I became a slave to his will and was ordered to protect and carry out McCullen's orders. After we fought in the Arctic base..." here he looked towards Snake again. "The nanomites healed up my wounds and I made my way to another base so that I could recover. I started to remember the true events of my past and realized that I had wronged you. So I decided to make it up to you. So I found as much evidence as I could and sent it to you." Storm Shadow stated.

"How do we know that was you? What were the initials that it was signed with?" General Hawk asked.

"The initials are of my name. As you know Storm Shadow is not my actual name but what many have called me even since I was young. The letter was signed TSA. Right?" Storm Shadow said looking carefully at the General.

"Yes. I wonder then if you would be willing to tell us your name?" Hawk asked carefully, knowing how secretive ninja were.

"Snake knows my name. But if you really want I will tell you, on one condition." Storm Shadow asked looking slightly apprehensive.

"Yes. What is it you wish to ask?" Hawk looked at the other Joes around the room, as they to wondered what the ninja assassin would want.

"Would you consider letting me become a member of your team to make up for the wrongs I have made against you?" Storm Shadow asked shocking all the Joes, even Snake Eyes.

"We will have to discuss it." Hawk said leaning forward thinking about this new development.

"Very well. Then I shall tell you my name then. My name is Thomas. S. Arashikage." Storm Shadow stated proudly.

"Arashikage. As in the clan you trained with was your family." Duke spoke for the first time.

"Yes. I am now the only surviving member. So I am considered the Arashikage heir. Arashikage translates as Storm Shadow which is the name you know my by. I can see by your shocked faces that Snake never told you." He smiled at his sword brother.

It was yours to tell, brother. Snake signed.

The others gasped a collective "What?" as Snake Eyes called him brother.

"Snake was adopted into my family. He became my brother. Another reason why I want to work with you is to make amends with you Snake." Thomas stated.

What happened after you sent us the data, Tommy? Snake signed getting back onto the story knowing that it was not finished.

Storm Shadow grimaced and told how he had been caught by Zartan and the days of torture he had endured for days after. Eventually Storm Shadow grew tired and the Doc and Lifeline asked them all to leave so that he could rest.

They left to go and discuss the possibility of Storm Shadow becoming a member of the GI Joes.

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The Joes and Hawk went to a briefing room to discuss Storm Shadows future. Would they arrest him and sentence him to death for killing innocent people or would they allow him to become a member of GI Joe. Indeed while people did not ask to be a part of GI Joe, ninja were very good soldiers.

"I don't think we should let him live or join us." Scarlett started immediately.

The Baroness agreed emphatically. "He has killed many of your team and many innocents have died because of him as well." She states in a cold voice. "He should not be forgiven for these crimes, nor should he be made a part of your team General."

You have done these things to. But we have forgiven you and let you become a part member of the team. Snake Eyes gestured, the anger showing in his sharp movements.

The Baroness glared at Snake Eyes quickly before conceding that he did have a point.

My brother is a trustworthy person. He was under the control COBRA. The Doc and Lifeline have confirmed that he did have nanomites in him and that they have been used to change his memory. Snake Eyes gestures slowly.

Hawk nods as he had received the same report, he had also been told about Storm Shadows actions after he had awoken and the way he had looked at Snake Eyes had been happy so Doc and Lifeline had told him. After several minutes more of discussion where the Baroness and Scarlett argued that Storm Shadow should not be trusted and Snake Eyes stuck up for his brother and the other Joes listened and made occasional comments, Hawk cleared his throat and got the all their attention.

"I think that after all the evidence presented by Storm Shadow and all of you, Storm Shadow will be allowed to show us that he has turned to our side." Hawk finished with a look at all of them, his look said not to argue.

The General had made up his mind to trust Storm Shadow due to the evidence and that the man had willingly told him the answers to his questions no matter how personal. He also trusted Snake Eyes' judgment.

Snake Eyes nodded happily at the General. They could all see his grin through his mask.

The rest of the team agreed that the General had made the right choice.

"Shall we go and tell him the good news then?" General Hawk stood and they all walked back to the medical bay.

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They walked into Storm Shadows curtained off section. Storm Shadow looked up and smiled when he saw Snake Eyes. Snake Eyes sped up happy to see his friend again and tell him the good news.

Hawk reached the pair. Storm Shadow looked at the General in the eye. Then Hawk smiled and held out his hand. "Welcome to GI Joe Storm Shadow." He said. He couldn't help but smile at Storm Shadows own smile.

Storm Shadow jumped out of the bed to the surprise of all the Joes, Doc, Lifeline and Hawk. He snapped a salute and then bended down on his knee pulling up the right arm sleeve of his uniform past his forearm. He revealed a tattoo on his arm. It was the same symbol that was on his and Snake Eyes swords and also on Snake Eyes uniform.

"This is the symbol of the Arashikage clan. I swear on the honor of my clan mark that I will serve you well and obey your orders. I will not betray you, Snake Eyes or your team as that would dishonor my clan and me." He looked at General Hawk, his face showing that he was serious about this.

Hawk knew that something like this was serious as Snake Eyes had done this when he was asked to GI Joe.

"Thank you Storm Shadow. I know that you will be a good asset and I know that you will be loyal to us. Like I said before, welcome to GI Joe. Just before I go, when you go on missions you will be a part of the Alpha team. You will partner with Snake Eyes if that is acceptable?"

Storm Shadow nodded. "Yes that would be absolutely fine and again thank you for giving me this chance when I have been your enemy for so long. I thank all of you." He said with a large smile, looking at all the Joes.

The other Joes could not help but smile at the enthusiasm Storm Shadow had and they all noticed that Snake Eyes himself already seemed a lot happier.

The Joes left with Hawk. Snake Eyes stayed with Storm Shadow.

You know if you want your swords, I picked them up and brought them back with me after our fight in the Antarctic. I know how much your swords mean to you. Snake Eyes gestured to his friend.

Storm Shadow's face lit up once again as he thought about the swords that were the last thing given to him by his master. They did indeed mean a lot to him and he was glad that Snake Eyes had them.

"Thank you my friend. Yes, I would like them back and thank you for taking care of them. By the way when I leave this ward, where will I be staying?" Storm Shadow asked smiling at Snake Eyes.

You will stay in my room with me as I don't have anyone to share with and not many people want to put up with ninja ways. Is that Ok? Snake Eyes gestured slowly as if thinking his offer would be refused.

Storm Shadow's grin only got wider. "It would be good to room with you again, brother." He exclaimed making Snake Eyes smile beneath his mask.

They both caught up on what each other had done over the years they had not known each other and they both realized that their friendship was very much intact and had been strengthened. Nothing could break the bond that had been made between the two now.

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It was a few weeks before Storm Shadow was finally let out of the Joes hospital ward. Snake Eyes appeared next to his friend and gestured for Storm Shadow to follow him to his quarters.

They reached the quarters that was to be theirs and entered. The first thing Storm Shadow noticed was that his and Snake Eyes' swords were together in a case meant to protect them. He slowly approached and withdrew his blades and looked over them with a professional eye noticing that his brother had indeed taken good care of the weapons; he turned and smiled his thanks to Snake Eyes. Snake Eyes just nodded in return.

The room was big enough for two military issue cots, wardrobes and enough room for the two to move around. There was also a bathroom attached.

It's not much, but to me it's like home. Snake gestured to his friend, as Storm Shadow had come from a rich and powerful ninja clan.

"I like it. I have stayed worse places. This is seriously amazing." Storm Shadow said as he looked around.

Snake Eyes had decorated the room to in part look like the Arashikage rooms. On his wall was a painting of the Arashikage symbol. Storm Shadow knelt before it, paying his respects. Then he got up and asked which his bed was. Snake gestured to the bed on the right and Storm Shadow nodded. He went and sat. Snake went to his own bed and they both sat in companionable silence.

"Thank you for believing me. I know that I have hurt you much over these last few years and I am really sorry." Storm Shadow spoke at last.

I knew that deep down you were good and I trusted that you would find your way. I was inconsolable after our battle in the Antarctic. But now you're back and we can be the team that we were when we were back home. I will always have your back, Tommy.

"And I will always have yours, Yamane" Storm Shadow said smiling at Snake Eyes.

Snake Eyes started in surprise at the use of his nickname. Storm Shadow had picked it because when they were young he did not speak much. It was also picked because he was younger than Storm Shadow and Storm Shadow protected and helped him so the nickname stuck. Snake Eyes also realized that he was overjoyed at the use of the name. He also noticed that for the first time since Storm Shadow had disappeared he had called him Tommy.


	2. Chapter 2

**Notes for the Chapter:**

> Note: The Alpha team now consists of: Storm Shadow, Snake Eyes, Heavy Duty, Breaker, Duke, Ripcord and Scarlett. The Baroness may sometimes accompany the team.

It had been a few weeks since Storm Shadow had been rescued and allowed to stay with the GI Joes. Many of the Joes were still suspicious of the former COBRA ninja, none more so than Scarlett. The Baroness was also making as much trouble possible for the newest addition to the team.

However Storm Shadow just ignored them. He had his brother back and was on the right side and that was all he needed and wanted.

Snake Eyes was also happy to have his old friend back and they would train, eat and spend most of their time in each other's company.

The rest of the Alpha team after seeing how happy Snake Eyes started to give Storm Shadow a chance, the same chance that they had given the Baroness after she changed sides and they made sure to make this known to the woman.

This led to Heavy Duty, Breaker, Duke and Ripcord to spend more time with the ninja. They all formed a close bond and became good friends.

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In a prison cell the Cobra Commander smiled behind his mask. No matter that the Joes had won this battle, the war was far from over and he had vowed that he would come out on top.

It was just a matter of time…

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As the next few days passed, the GI Joes got word that COBRA was mobilizing for a big mission.

"Ok Alpha team, this is what we have heard; the COBRA troops are starting to gather, under whose order I don't know. We believe that they aim to free the Commander and McCullen aka 'Destro'. We must not allow this to happen." Hawk briefed the Alpha team as well as the Baroness.

"I know who is organising them." Storm Shadow told the group as they studied maps of the prison that help the Commander and Destro.

Who is it? Snake Eyes signed.

"The man who tortured me after he found me sending the information to you. His name is Zartan. I can't tell you much about him. He kept himself to himself." Storm Shadow's voice held traces of e the anger he felt burning inside.

"Can you give us a description so that we know who we are looking for?" Hawk asked watching the Arashikage Heir.

"Yes." Storm Shadow answered and proceeded to tell the team Zartan's appearance. "He is also a master of disguises. He was with us when we came for the warheads; he was the one who stabbed the lady lieutenant."

Hawk looked towards the Baroness who nodded reluctantly. Hawk also vaguely remembered the man who had killed the loyal lieutenant.

"Thank you Storm Shadow." Hawk said. "Now we have some idea of who we are looking for. We have to stop him and the COBRA soldiers from freeing the Commander and Destro."

The team proceeded to plan how to defend the prison against the possible escape attempt.

The contributions of Storm Shadow and the Baroness being very helpful as they knew COBRA's tactics.

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It was nearly time, it would happen soon.

"Prepare yourself Destro, for soon we will be free and the Joes will regret that they ever crossed me" and with that the Cobra Commander laughed ominously and darkly as Destro murmured "Yes Commander."

"All the pieces are in place and soon this world will be under MY control and I will have revenge on Duke and those ridiculous Joes."

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The Joe's were staged at the posts across the prison. Storm Shadow and Snake Eyes were partnered together close to Destro and the Commander's prison cell. They had a good view of the courtyard and of the corridors on their level as well as the corridors below.

Duke and the Baroness were station right outside the Commander's Cell with Destro's being the one on the right of the Commander's.

Heavy Duty and Breaker were in the security room which was on the ground floor with the courtyard watching the cameras.

Ripcord and Scarlett were on the roof.

This was so that they could cover all the exit points.

The two ninja being close to the Commander in case he managed to get out or away and needed to be neutralised.

Their backup was a couple of miles away in their specially designed planes.

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"It begins…Now!" The Commander's voice echoed through his cell.

Duke and the Baroness turned towards the cell curiously to observe the commander standing, his back military straight and hands clasped in front, his eyes burning with hatred through his serpentine mask.

Duke and the Baroness' coms had picked up what the Commander said and the team's prepared themselves to fight.

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"Are you ready brother?" Storm Shadow asked Snake as he drew one of his white swords from their sheaths on his back.

I am. Good fighting brother, and be careful. 

"You too." Storm Shadow whispered to Snake knowing the man would be able to hear him.

Snake nodded and drew his own sword. Storm Shadow heard approaching planes and cars and quickly told Snake Eyes and the rest of the team.

"There seems to be 4 of the COBRA planes, like the one we travelled in approaching from the north, east, south and west and there seems to be at least 5 military style trucks pulling up at the gates." Storm Shadows extra sensitive hearing could also make out the slight sound of heartbeats. "All of them have soldiers inside. Overall I would say there are at least 30 to 40 COBRA soldiers headed towards us." As Storm Shadow finished speaking there was a loud explosion on the left side of the building, close to where Storm and Snake were. It knocked them both to the floor, Snake recovering first and jumped to his feet and looked at the cells down the corridor on the left. In around about the middle group of cells there was a large hole that was spattered with flames here and there.

Snake helped Storm Shadow up knowing that the sound of the explosion so close to him would have hurt his ears.

Are you okay? He signed quickly worried about his best friend.

"I'm fine." Storm Shadow groaned as he managed to stand on his own and shook his head.

There was another explosion at the other end of the prison as the planes circled around the large rectangular prison.

It was then that all hell broke loose as the vehicles smashed their way and two of the planes managed to land long enough to drop its contingent of soldiers.

In their coms they could hear Hawk yelling for the back-up to get to the prison and help the Alpha team.

Storm Shadow and Snake Eyes looked at each other and nodded. They could handle this.

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In his cell the Cobra Commander laughed as Duke and the Baroness were engaged in battle. He moved to stand closer to the cell door.

"Looks like you're going to lose. You never should have crossed me." His deep baritone voice hissed.

"I will get my freedom…"


	3. Chapter 3

The military vans that crashed through the gates of the prison came to a stop in the prisons courtyard. The doors opened as Heavy Duty and Breaker were taking cover to begin the fight. In their coms they could hear Scarlett and Ripcord shouting warnings to each other as they too came under attack.

From the Cobra Commander's prison level, Snake Eyes and Storm Shadow were targeting the Cobra Vipers with the guns that Snake had brought. Storm Shadows shuriken would not do much damage from their height, so he used his SIG-Sauer P226 Sport II whilst Snake Eyes used his FN FiveseveN. Both were excellent shots and managed to hit a number of the Vipers, however they were aware that there were more above.

Scarlett and Ripcord were outgunned and outmatched. There were 20 Vipers on the roof, and very limited cover. Adding to this were the Cobra weapons which were highly destructive, meaning that the cover the pair took only took 3 hits before disintegrating.

"We have to move for the door. If we can get them to bottleneck it might make it easier for use. Up here there is too much space for them to move around and get us." Scarlett shouted to Ripcord as she jumped from her cover as it was blasted apart.

Aiming her crossbow, she fired straight at the eye piece of the Viper's mask. The Viper's head exploded with a miniature blast.

Ripcord agreed as he fired his assault rifle at 2 of the approaching vipers.

They both met up as close to the door as they could, whilst still avoiding the pulse blasts from the Vipers weapons. Ripcord then threw a flash bang grenade in the middle of their opponent's arrow like formation.

"1…2…3…Now!" They both darted to the door as the flash bang exploded; causing the Vipers to cover the eyes of their masks.

As they ran they fired several rounds, taking down several of the Vipers. If the Vipers were dead or simply wounded, they did not know.

"Can you make a miniature bomb?" The question sounded in their coms.

"What?" Scarlett asked pressing the com closer to her ear.

Storm Shadow's voice came through again: "Do you have some frag grenades and string? The Vipers masks restrict some of their vision making it harder for them to see something like wire across stairs."

Scarlett quickly located some wire that she and most soldiers kept in case of emergencies. "I've got it."

"Good, now tie the wire to the pin of the grenade. You then need to tape or find somewhere to wedge the grenade so that it won't be pulled; we only need the pin to come out. Then find a place to attach the wire across from the grenade, so it forms a tripwire." Storm Shadow advised, startling Scarlett with the simplicity of the plan.

Ripcord tied the string and wedge the grenade into a tight corner of the stairs, giving a small experimental tug on the wire to make sure the grenade would not roll out. He then dragged the wire directly across from the grenade and located a small nail, which he promptly tied the wire around; making sure that the wire was taut enough to trigger the trap.

"Ok, it's set." Ripcord spoke quietly.

Get to cover. If there are still too many, come and join us. We need help to back up the others, they have managed to reach this level. Snake Eyes tapped Morse code on his own com device.

"Ok, moving to cover now, and then we'll join you in 5 minutes once we have determined how many are left." Scarlett stated calmly as she and Ripcord made their way down the rest of the stairs and out of the door, taking cover either side.

The trap had been set in the middle of the staircase to allow as many Vipers into the stairway as possible.

After waiting for at least another 30 seconds, while the Vipers recovered from the after effects of the flash bang, they heard boot steps marching down the stairs.

Pulling their heads back slightly as the lead Viper made it to the grenade; they tensed themselves waiting for the inevitable explosion.

BOOM!

The grenade blasted bits of concrete down the stairs.

Quickly checking their weapons, Ripcord and Scarlett peaked out from their cover and saw the stair way was completely obliterated. They could make out some of the remains of the Vipers, while others had been crushed by cement falling from above.

Looking at the doorway at the top of the stairs they saw 6 Vipers staggering to their feet and collecting their weapons.

The rest were dead.

"We should be able to take them. There are only 6 left." Scarlett whispered to Ripcord who nodded.

They exited their cover and just as they started to take aim at the Vipers, one of them turned with a cylindrical device in his hand.

He pushed a button that was on top of the device and threw it down at the pair.

Realising it was a grenade of some sort, Ripcord and Scarlett jumped to their left, just as the grenade hit the floor they were on.

They quickly ran as far as they could when the grenade let out a psionic boom. It caused the floor beneath them to quake and in some areas to fall to the level below.

The shockwave of the grenade, even though they were some meters away forced the pair forward, smashing them against the bars of one of the cells.

"We need to get to Snake and Duke." Ripcord said as they raised up their bruised and battered bodies.

Scarlett nodded and together they limped in the direction of Snake Eyes, Storm Shadow, Duke and the Baroness.

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Meanwhile the Duke and the Baroness were also sniping the Vipers that were in the courtyard. They could hear the sounds of the two ninja engaging in hand to hand with the Vipers that had made it to the Commander's prison cell level.

"Oh my…It sounds like quite the battle out there, doesn't it?" The Cobra Commander hissed sibilantly, amusement ringing through his words. "Are you ready for defeat yet?"

"They can't help you Rex. We won't let you get away from here." Duke stated, confident in their ability to keep the crazed genius behind bars.

"If you think I won't get out of here, then you are a fool. I've been planning this ever since you caught me." Cobra Commander hissed victoriously, absolutely certain that his plan was fool proof.

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Storm Shadow and Snake Eyes were using all of their skills as ninja to avoid the gun fire from the Vipers. They were ducking, weaving and even flipping through the air as they took down as many of the Vipers, using swords, guns and shuriken. But somehow a force of 12 Vipers, 5 of which were the nanomites enhanced Neo-Vipers, had made it to the Commander's level. So far only 2 of the Vipers and 1 Neo-Viper had been dispatched.

"I don't think we can hold on for much longer here. We need back up." Storm Shadow shouted to his brother as he thrust his sword through one of the Vipers armoured chests.

The Viper fell to the ground dead, only to be replaced by another who was already firing his pulse rifle.

General Hawk says backup will be here in 1 minute and 30 seconds. Snake quickly tapped on Storm Shadows back as the two briefly took cover behind a corner, using the wall as a shield.

"We may not be here in a minute. Where are Ripcord and Scarlett? I thought they were joining us. It has been longer than 5 minutes." Storm Shadow whispered, concern slipping into his voice.

Literally a second after he asked, Scarlett and Ripcord made their appearance, right behind the Vipers who were making their way towards the 2 ninja.

The 4 stared at each other before swiftly moving into action. They attacked the remaining Vipers from the front and back, taking the remaining Vipers by surprise, giving them very little time to attack.

Storm and Snake fought back to back making sure to cover each other at all times, just like they had been trained too when they were younger.

Within minutes the surprised enemies had fallen to the 2 experience ninja, ninja in training (Scarlett) and Ripcord.

"Heavy, Breaker, how are things down in the courtyard?" Scarlett spoke into her com as Snake Eyes made gestures for them to join Duke and the Baroness.

"It's all good; we have wiped out most of their forces. There are only 4 more down here, but there sure as hell is a lot of damage done to this place. It's good that the other prisoners and staff were evacuated." Heavy Duty's slightly weary voice came through the coms.

"Duke, how about you and the baroness, you ok?" Ripcord asked worried about his friend.

"We're fine here too, they never got near here." Duke's voice was calm through the com.

"We're coming to you. The backup should be here in under a minute." Scarlett stated.

Storm Shadow, Snake Eyes, Scarlett and Ripcord made their way to Duke, the Baroness and the Cobra Commander, unaware that the attack had not yet finished.

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"Looks like your plan failed, Rex." Duke said to the masked man as he moved to stand in front of the cell.

"Is that what you think? That was just the first phase. Now it's going to get much harder." The Cobra Commander laughed darkly, his mask distorting the sound, making it much deeper and raising Goosebumps on Duke's and the Baroness' skin.

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"DOWN!" Storm Shadow yelled as he jumped, pushing Snake Eyes to the round while Scarlett and Ripcord just reacted to the order and dropped onto the stomachs.

The walls of the cells were disintegrated as the 4 Cobra helicopter blasted the walls with their pulse cannons.

"What are they doing, they could kill the Commander?" Ripcord shouted over the noise of the cannons destroying another cell's walls.

"No, they won't. We have to move. Now!" Storm Shadow shouted as he jumped to his feet and quickly helped the others to theirs.

"What's going on?" Ripcord demanded as they ran towards the Cobra Commander's cell.

"If I know the Commander well enough, and I do, then the only reason he would do something like this is if he has a way of not being in his cell. He wouldn't take risk like this if he wasn't certain he couldn't get out. DUKE!" Storm Shadow shouted into his com.

However there was no response.

Storm Shadow and Snake Eyes quickened their run.

The four arrived outside the Cobra Commander's cell to find the door had been blasted off of its hinges from the inside.

The Cell was empty and so was Destro's.

"Where's Duke…and the Baroness?" Scarlett asked as she looked around the rubble in front of the cells.

"Over here." They heard Duke's voice come from over the railing looking over into the courtyard.

Looking over it, Snake and Storm found Duke holding on with one had while his other held the Baroness' hand.

They both looked fine other than a few scratches, scrapes and bruises.

Storm and Snake reached over and grabbed hold of Duke's hand, and along with Ripcord and Scarlett, they managed to pull the 2 up.

"What happened?" Heavy Duty's voice asked as he and Breaker arrived on the same level.

"Rex escaped; somehow he had one of those pulse pistols. Or something like it. I'm not sure." Duke groaned as he and Baroness were pulled to safety.

"He got us to come closer to his cell and then pulled the gun and pulled the trigger. It was powerful enough to blast the cell door and push us over the rails." Baroness gasped.

At that moment the backup GI Joe troops drove in through the busted gates.

Did you see in which direction he went? Snake signed to Duke.

"To one of the cells that helicopter's had blasted a hole through." Duke pointed to one of the closest cells that had no wall.

"It was all a setup, sending those soldiers in made us think they were going to rescue him when he had planned this all along. This battle was nothing more than a diversion to split us up while he made his true escape, and if he killed us all in the process then all the better." Storm Shadow explained as it dawned on him what the Cobra Commander's plan had been all along.

"He is definitely one hell of a strategist." Heavy Duty spoke, a small amount of admiration for the daring plan in his voice.

One of the GI Joe soldiers reached them. "We have searched but have located nothing to indicate how the Commander was able to get a weapon or to indicate where he is going. We lost track of the helicopters when the jammed our scanners."

"Alpha team, you are to report back at the Pit, at once. There's nothing more we can do now. You did good, but even I never saw this coming." General Hawk's calm voice came through the coms.

"Yes sir, and we're sorry for losing him sir." Duke replied, shame in his voice for losing the genius terrorist.

"Don't worry about it, we caught him once and we will again. Come back in guys." Hawk then cut off communication.

The team made their way to their transport and started to take care of the wounds they had received.

Hours later they arrived at the Pit, all thinking about what had happened and what would happen next.

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"Hello Zartan." The Cobra Commander's deep hissing voice echoed around the office of the President of the United States.

Zartan looked at the President's desk where the Commander sat, straight backed, with Destro on his right like some sort of bodyguard.

"Commander." He whispered bowing his head in respect to the genius.

"Now, it is time to make the Joes and the world mine." And with that the Commander through his head back laughing psychotically.

Everything was now under his control.

**Author's Note:**

> Yamane – translates as dormouse. This is from the Google translator and I hold no responsibility if it is wrong. I thought it would be good nickname for Snake Eyes as he is quiet; also I wanted to give them something from a friendship. I also like the idea of thinking that Snake Eyes could be a couple of months younger than Storm Shadow.


End file.
